| Literature DB >> 35140695 |
Hamed Azarbad1, Julien Tremblay2, Luke D Bainard3, Etienne Yergeau4.
Abstract
Next-generation sequencing is one of the most popular and cost-effective ways of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are limited, as they result in relative abundance profiles of microbial taxa, which does not represent actual abundance in the environment. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that changes in the relative abundance of major microbial phyla do not necessarily follow the same pattern as the estimated quantitative abundance. Most of the bacterial phyla linked with the rhizosphere of plants grown in soil with no history of water stress showed enrichment patterns in their estimated absolute abundance, which was in contradiction with the trends observed in the relative abundance data. However, in the case of the fungal groups (except for Basidiomycota), such an enrichment pattern was not observed and the abundance of fungi remained relatively unchanged under different soil water stress history when estimated absolute abundance was considered. Comparing relative and estimated absolute abundances of dominant bacterial and fungal phyla, as well as their correlation with the functional processes in the rhizosphere, our results suggest that the estimated absolute abundance approach gives a different and more realistic perspective than the relative abundance approach. Such a quantification approach provides complementary information that helps to better understand the rhizosphere microbiomes and their associated ecological functional processes.Entities:
Keywords: amplicon sequencing; microbiome; qPCR; quantitative; stress history
Year: 2022 PMID: 35140695 PMCID: PMC8819139 DOI: 10.3389/fmicb.2021.798023
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
FIGURE 1The abundance of (A) bacterial 16S rRNA gene (copies g– 1 soil dry weight) and (B) fungal ITS region (copies g– 1 soil dry weight) in the rhizosphere of four wheat genotypes grown in soil with two contrasting stress histories (Soil history) under different contemporary water stress (SWHC).
FIGURE 2The effect of soil history on (A) the relative and (B) estimated absolute abundance of different bacterial phyla associated with the rhizosphere of four wheat genotypes grown in Saskatchewan soils with a water stress history (NI) or with no history of water stress (IR) exposed to four levels of soil water content. Dots are values for individual observations, the horizontal lines in boxes are representative of the median, the upper and lower part of boxes indicating 75th and 25th quartiles, and whiskers on the boxes showing 1.5 × the interquartile range. ANOVA tests comparing the abundance of each phylum between IR and NI soils.
FIGURE 3The effect of soil history on (A) the relative and (B) estimated absolute abundance of different fungal phyla associated with the rhizosphere of four wheat genotypes grown in Saskatchewan soils with a water stress history (NI) or with no history of water stress (IR) exposed to four levels of soil water content. Dots are values for individual observations, the horizontal lines in boxes are representative of the median, the upper and lower part of boxes indicating 75th and 25th quartiles, and whiskers on the boxes showing 1.5 × the interquartile range. ANOVA tests comparing the abundance of each phylum between IR and NI soils.
Correlation tests between relative and absolute abundances of the most abundant bacterial phyla associated with the rhizosphere of four wheat genotypes grown in Saskatchewan soils with a water stress history (NI) or with no history of water stress (IR) exposed to four levels of soil water content vs. CO2 production.
| CO2 production | ||||
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| Relative abundance | Quantitative abundance | |||
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| Acidobacteria | 0.158 |
| 0.101 | 0.208 |
| Actinobacteria | –0.361 |
| 0.040 | 0.615 |
| Bacteroidetes | –0.036 | 0.656 | 0.061 | 0.451 |
| Firmicutes | –0.079 | 0.327 | 0.051 | 0.528 |
| Gemmatimonadetes | 0.272 |
| 0.104 | 0.193 |
| Proteobacteria | 0.277 |
| 0.093 | 0.249 |
| Verrucomicrobia | 0.071 | 0.378 | 0.078 | 0.331 |
Bold P-values are significant at P < 0.05.